I am using ANNOVAR to annotate WGS SNPs with default parameters, and I get two output files, variant_function and exonic_variant_function. The variant_function file contain "downstream,exonic,intergenic,intronic,ncRNA_exonic,splicing,upstream,UTR3,UTR5" and I know the exonic_variant_function file has more detailed annotation for exonic, "synonymous,nonsynonymous,stopgain,stoploss,unknown". Then I change the parameter "-precedence", make "ncRNA" be the last one, and now the output contain "downstream,exonic,intergenic,intronic,splicing,upstream,UTR3,UTR5", the "ncRNA_exonic" are annotated to be "exonic".
My question is when I change the "-precedence", the exonic_variant_function has no change, it's the same as before. I want to know how can I make the exonic_variant_function file contain the added "exonic". Any suggestion is appreciated. Thank you very much in advance.
